The present thesis deals with the phenomenon of additional sex chromosomes in Cimex lectularius (Hemiptera: Heteroptera: Cimicidae) using genome size analysis combined with the classical cytogenetic approach. Also, five other cimicid species and 12 species from the family Nabidae were analysed identically for comparative purposes. The thesis also pursues a description of methodical approaches of cytogenetics and flow cytometry in the study of C. lectularius. Recently analysed European specimens of C. lectularius from human host exhibited 12 distinct cytotypes, with a variable number of chromosomes X from two to 20 (2n♂ = 26+X1X2Y to 26+X1-20+Y). The fragmentation hypothesis of C. lectularius additional chromosomes X origin was established in the second half of the 20th century. However, the present genome size measurements suggest that various chromosomal rearrangements as duplication or deletion besides the fragmentation could occur. Males with basic cytotype 2n = 26+X1X2Y had average genome size of 2C = 1.94 pg, in contrast male with 2n = 26+X1-7+Y yielded 2C = 2.26 pg and also specimens with genome size decrease 2C = 1.69 pg appeared. The most informative turned up to be the relative genome size of sperm cells n = 13+X1X2 and n = 13+Y, where specimens with higher chromosome number showed...

<p>Due to Ireland’s secluded geographical location, its genetic structure is a popular topic of study. The indigenous inhabitants of Ireland remained undisturbed for a long period time, allowing for a distinct genetic population to be created. This peace was disrupted by conflict with invading forces, such as the Nordic Vikings and Anglo-Norman forces. However, these historical events helped to shape both the culture of Ireland and the ancestry seen in the Irish population today. In Ireland, quite like many countries around the world, the male’s surname is passed from father to son, just as the Y-chromosome. The relationship between Irish surnames and their corresponding Y-haplogroups was examined to determine if common and rare Irish surnames can be genetically linked to the historical invasions listed above. The surnames chosen for this study were selected based on their prevalence in Ireland, rare or common, and their proposed historical origin, Irish, Norse or British. To discover any possible patterns in surnames and Y-chromosomal DNA, Y-haplogroups were generated from the DNA of 630 Irish male subjects using an assay specifically developed for the region. The assay contains twenty single-nucleotide polymorphisms (SNPs) that were selected to further resolve the R1b-L21 Y-haplogroup for Irish ancestry, the most prevalent haplogroup in Western Europe, and Ireland in particular. Additional Y-STR data was also generated to examine recent surname history within the collected individuals. Each surname was examined to determine whether one haplogroup occurred more frequently and with this method, distinct patterns in Irish surnames and geographical locations were discovered. In addition to resolving Y-surname history patterns, it is also believed that this assay may be beneficial in determining if an unknown DNA sample is of Western European origin and even in some cases, if a more specific Irish origin can be predicted.</p>

Comparative cytogenetics of the bed bug Cimex lectularius (Heteroptera: Cimicidae) The human bed bug Cimex lectularius has started enormous spreading to all developed countries of temperate climate zone during the last ten years. Bed bug was almost eradicated by a mass use of DDT in these areas until the 70's in the 20th century. This temporal haematophagous ectoparasite occupies particularly human dwellings and bat roosts. Cimex lectularius shows unusual combination of cytogenetic characteristics, general for all Heteroptera, however, not usual for other organisms. The chromosomes are holokinetic, with completely achiasmatic meiosis and inverted meiosis of the sex chromosomes. Especialy remarkable feature is intraspecific variation of the number of the X chromosomes. The variable number of chromosomes of 43 populations of Cimex lectularius from the Czech Republic and 27 populations from other European countries was studied in the present study. The 10 variants of karyotype were found out by using the "hotplate spreading" method and the standard Giemsa staining. There were male karyotypes with 2n = 29, 30, 31, 32, 33, 34, 35, 37, 42 and 47 chromosomes and two females with peculiar odd number of sex chromosomes X, 2n = 33 and 43, not complementary with any male. A stable number of 2n = 26 autosomes...

Evolution of sex determining mechanisms in squamate reptiles (Reptilia: Squamata) Martina Pokorná Ph.D. thesis Abstract This Ph.D. thesis is focused on the evolution of sex determining mechanisms and genomes in squamate reptiles. It is based on three published articles and two manuscripts. The evolution of sex determining mechanisms, sex chromosomes and genomes, and their organisation, was studied on a wide phylogenetic scale of the whole group of squamate reptiles and some lineages of other Sauropsids, as well as on the small phylogenetic range as a detailed comparative study inside individual lineages of squamates. This thesis is based upon the use of classical cytogenetic methods, methods of molecular cytogenetic (especially fluorescent in situ hybridisation) and the results were analysed using phylogenetic approaches. The results and outputs of this study represent an important contribution to the general knowledge of the principals of sex determination and the evolution of these phenomena not only in squamate reptiles but also in the whole group of amniotes. Using the results obtained during the work on this thesis we can conclude that sex chromosomes evolved in particular lineages of amniotes independently. This origin was in some cases followed by accumulation of microsatellite sequences on sex...

Snakes (Serpentes) are a group of squamate reptiles (Squamata) including more than 3600 species. The vast majority of snakes are from the group Caenophidia, which includes approximately 90% of all extant snake species and represents the most studied lineage. Squamate reptiles are variable in sex determination and genome organisation, however, caenophidian snakes are quite stable in these respects. The typical - and probably ancestral - snake karyotype is composed of 36 chromosomes with 16 macro- and 20 microchromosomes. In all snake species, genotypic sex determination (GSD) is expected and it was assumed until recently that all snakes possessed ZZ/ZW sex chromosomes. The main reason for this is that most of the studied snakes were from the group Caenophidia and in the rest of the snake lineages it was believed that their sex chromosomes were homologous. In fact, the sex chromosomes of non-caenophidian snakes have not yet been identified - with the single exception of Acrantophis dumerili. Nevertheless, a recent study showed that there was an independent evolution of XX/XY sex chromosomes in pythons and boas. Sex chromosomes of these snakes are homomorphic and so far they have not been detected by classical cytogenetic methods. In this context, the aim of this study is to explore whether it is...

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

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<p>Sex chromosomes have evolved independently multiple times in plants and animals. Sex chromosome evolution theory predicts the gradual degeneration of the sex-specific sex chromosome due to suppression of recombination, which lowers the efficacy of natural selection. Suppressed recombination also acts to resolve sexual conflict and ensure proper segregation of sex-specific alleles. However, sex chromosome degeneration is not always the case, and evolutionarily old, and young, but homomorphic (nondegenerate) sex chromosomes have been observed. African clawed frogs (<em>Xenopus</em> and <em>Silurana</em>) have homomorphic sex chromosomes due to a recent turnover event. However, occasional recombination between the sex chromosomes may contribute to the maintenance of homomorphic sex chromosomes in African clawed frogs. Mechanisms that prevent divergence of sex chromosomes may be related to polyploidization, which is frequently observed in African clawed frogs. The studies herein construct a phylogenetic framework to test alternative hypotheses for selection on sex-linked and autosomal genes involved in sex determination, map sex chromosomes and compare sex chromosomes across African clawed frogs. I have also explored the relationship between phenomena like recent turnover events, recombination and polyploidization to sex chromosome degeneration (or lack thereof). In this dissertation, I have discussed the potential for multiple mechanisms of sex determination and the unique pseudoautosomal nature of sex chromosomes within this group of frogs. This body of work provides a comprehensive study of sex chromosomes in a group lacking phylogenetic resolution and sheds light on the origin and evolution of sex chromosomes in other organisms.</p> / Doctor of Philosophy (PhD)

Despite the advances in modern technology, unraveling the genome evolution of an organism or even groups of several species remains a challenging task. Up-to-date cytogenetics and computational approaches enable the investigation of genomes from the nucleotide sequence up to the chromosomes, yet, drawing conclusions about evolutionary and mechanistic processes remains far from being trivial. The crop sugar beet (<i>Beta vulgaris</i> subsp. <i>vulgaris</i>) and its wild relatives form a well-suited group of plants (members of the Amaranthaceae family) to demonstrate the possibilities and limits that both, cytological and computational genomics, possess in addressing open questions on the genome in a phylogenetic context and in all its conformations: from its organization in chromosomes right down to the loss and gain of genes and the composition of repetitive DNA sequences. Since the two beet genera <i>Beta</i> and <i>Patellifolia</i> comprise diploid as well as polyploid species, genomic variability between them is not only based on DNA sequence differences, but on changes in the chromosome number as well. In the frame of this work, using microscopic approaches (outlined in chapter II), it was determined that all beets share a base chromosome number of x = 9. Differing properties between cultivated and wild beet accessions are the result of polyploidization and changes in the DNA sequence rather than a restructuring of the chromosomes. In chapter III, the focus is on the tetraploid wild beet <i>Beta corolliflora</i>, whose polyploidization likely led to the development of many tolerances against adverse environmental conditions. Since its ancestry remained unresolved for a long time, five different bioinformatics tools have been developed and complemented with cytogenetics to unravel its parental relationships. As an ‘autopolyploid’ hybrid descending from closely related <i>Beta macrorhiza</i> accessions, <i>B. corolliflora</i> occupies an intermediate position within the spectrum of auto- to allopolyploidy. Today’s breeding endeavors aim for the (re-)introduction of genes from wild beet into cultivated beet accessions to improve crop species in the face of changing cultivation conditions. Yet, such efforts are impeded due to crossing barriers, reflected in the separation of the beet species into three distinct gene pools. Chapter IV aims to identify repetitive DNA sequences that may be involved in speciation and formation of these gene pools. For this, genome data has been generated for a panel of 17 different beet accessions and was analyzed bioinformatically as well as experimentally, using long and short read technology, fluorescent <i>in situ</i> and Southern hybridization. The overall repeat content was found to correlate with the beet genome sizes and whereas some repeats are well conserved among the beet species, the specificity of others mirrors the split into the three beet gene pools. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools with uniform centromeres in the primary and tertiary gene pool and patchwork centromeres in the secondary gene pool, likely contributing to the barriers in beet breeding. Furthermore, endogenous sequences of viral origin were also detected in all beet genomes with specific elements for the different beet gene pools. As for <i>B. vulgaris</i>, these endogenous pararetroviruses were found to contribute to the host’s defense against other (putatively harmful) viruses (chapter V). In summary, this thesis demonstrates the synergistic potential of integrating computational and cytological genomics for a comprehensive genome analysis of beets that can be transferred to any other species panel. Combining both approaches enables to unlock a deeper understanding of the genetic makeup and evolution of the species of interest, in particular with regard to the impact of repetitive elements. / Trotz des technologischen Fortschritts bleibt die Entschlüsselung der Evolution eines Genoms oder gar der Genome mehrerer Arten eine anspruchsvolle Aufgabe. Moderne zytogenetische und computergestützte Ansätze ermöglichen die Untersuchung von Genomen von der Nukleotidsequenz bis hin zu den Chromosomen. Trotzdem ist es alles andere als trivial, daraus Rückschlüsse auf evolutionäre und mechanistische Prozesse zu ziehen. Die Zuckerrübe (<i>Beta vulgaris</i> subsp. <i>vulgaris</i>) und ihre wilden Verwandten stellen eine Pflanzengruppe aus der Familie der Amaranthaceae dar, die sich gut dafür eignet, Möglichkeiten und Grenzen der zytologischen sowie computergestützten Genomik aufzuzeigen. Bei der Beantwortung offener Fragen zum Genom in einem phylogenetischen Kontext werden dabei all seine Ausprägungen in Betracht gezogen: von der Genomorganisation in Chromosomen bis hin zum Verlust und Erhalt von Genen und der Zusammensetzung repetitiver DNA-Sequenzen. Da die beiden Rübengattungen <i>Beta</i> und <i>Patellifolia</i> sowohl diploide als auch polyploide Arten umfassen, beruht die genomische Variabilität zwischen den Rübengenomen nicht nur auf Unterschieden in der DNA-Sequenz, sondern auch auf Veränderungen in der Chromosomenzahl. Im Rahmen der vorliegenden Arbeit wurde mit Hilfe mikroskopischer Methoden (siehe Kapitel II) festgestellt, dass alle Rüben eine Basischromosomenzahl von n = 9 aufweisen. Unterschiedliche Eigenschaften zwischen kultivierten und wilden Rüben-Akzessionen sind das Ergebnis von Polyploidisierung und Veränderungen in der DNA-Sequenz und nicht von chromosomalen Umstrukturierungen. In Kapitel III liegt der Fokus auf der tetraploiden Wildrübe <i>Beta corolliflora</i>, deren Polyploidisierung wahrscheinlich zahlreiche Toleranzen gegenüber widrigen Umweltbedingungen bedingt. Da ihre Abstammung lange Zeit ungeklärt blieb, wurden fünf verschiedene bioinformatische Methoden entwickelt und zytogenetisch komplementiert, um die Elternspezies zu entschlüsseln. So handelt es sich bei <i>B. corolliflora</i> wahrscheinlich um eine „autopolyploide“ Hybride, die von eng verwandten <i>Beta macrorhiza</i>-Akzessionen abstammt und eine Zwischenform im Spektrum der Polyploidie darstellt. Heutige Züchtungsansätze zielen auf die (Wieder-)Einführung von Genen aus Wildrüben in kultivierte Rübensorten ab, um die Kulturarten angesichts der sich ändernden Anbaubedingungen widerstandsfähiger und/oder ertragreicher zu machen. Solche Bemühungen werden jedoch durch Kreuzungsbarrieren eingeschränkt, die sich in der Gruppierung der Rübenarten in drei verschiedene Genpools widerspiegeln. Kapitel IV zielt darauf ab, repetitive DNA-Sequenzen zu identifizieren, die möglicherweise an Adaption und Artbildung beteiligt sind. Genomdaten wurden für 17 verschiedene Rüben-Akzessionen generiert und sowohl bioinformatisch als auch experimentell mittels Fluoreszenz-<i>in situ</i>- und Southern-Hybridisierung analysiert. Der Gesamtgehalt an repetitiven DNA-Sequenzen korreliert mit der Genomgröße der Rübenakzessionen. Während einige repetitive DNA-Sequenzen zwischen den Rübenarten konserviert sind, spiegelt die Spezifität anderer die Aufteilung in die drei Rübengenpools wider. Insbesondere die Satelliten-DNA variiert beträchtlich zwischen den Rübengenomen, was zur Entwicklung unterschiedlicher chromosomaler Strukturen in den drei Genpools geführt hat: Der primäre und tertiäre Genpool sind hierbei durch einheitlichen Zentromere gekennzeichnet, während sich der sekundäre Genpool durch eine individuelle Zentromerzusammensetzung auszeichnet, die von Chromosom zu Chromosom verschieden sein kann. Dies trägt wahrscheinlich zu den Hindernissen im Zuge der Rübenzucht bei. Außerdem wurden in allen Rübengenomen endogene Sequenzen viralen Ursprungs nachgewiesen, die für die verschiedenen Rübengenpools spezifisch sind. Für <i>B. vulgaris</i> wurde festgestellt, dass diese endogenen Pararetroviren zur Verteidigung gegen andere (ggf. schädliche) Viren beitragen (Kapitel V). Zusammenfassend zeigt diese Arbeit das synergistische Potenzial einer Integration der computergestützten und zytologischen Genomik für eine umfassende Genomanalyse von Rüben auf, die auf jedes andere Artenpanel übertragen werden kann. Die Kombination beider Ansätze ermöglicht ein tieferes Verständnis des Genoms und der Evolution der betreffenden Art, insbesondere in Hinblick auf den Einfluss repetitiver DNA-Sequenzen.